Hidden Agenda
by Tishbing
Summary: With Kirk's second year at the academy comes new and unexpected challenges. Section 31 has begun to show an interest in her. Her shipboard training is set to begin sooner than she expected. The Axanar peace and relief mission has more to it than what meets the eye. And with McCoy pressuring her for more things are almost too much to handle. Femkirk/McCoy seq. to "Don't I Know You?"
1. Chapter 1

Chapter One

It's so cold. She's always hated the cold but with the added hunger that claws at her insides it just makes it worse. The young man who's with her just adds to her irritation. Jim doesn't understand how he made it so far in his academy training. He's been difficult to deal with at the best if times but now it's almost impossible to remain civil with him. He didn't ration like Jim and as a result she had to share her supply, balked at the edible fungi and flowers that she had located for food. He wouldn't eat until Jim had located some berries and caught a fish the next day. He complained about everything. The most irritating had been when he had whined about not having clean clothes. Jim had shoved him into the creek they had been collecting water from after that.

"Why is it we're traveling at night?" John Albright rolls his eyes but continues to follow her.

"Because we're trying to avoid capture and get to the checkpoint. We're less likely to be spotted at night. Now shut up and keep your ears open." She hissed and threw out her hand to stop their movement.

The dark made the shadows loom and the trees surrounding them seem to move in the moonlight. It was playing tricks on her eyes. Jim's grateful they're in a forest rather than the desert or the arctic. She's always hated the cold. A crack sounds from behind them and immediately Jim tenses. She'd been so careful about leaving tracks.

"Come on!" Whispering urgently, she drags the man with her and shoves him down to the ground. Quickly covering him with dead leaves, she moves a few feet away and covers herself and waits.

It wasn't long before she saw the men hunting them. One was at least six feet with long black hair tied back, his large hands were holding a phaser rifle and a scowl was etched on his tanned face. His companion was smaller but not by much. He was dark skinned and thick muscled. Both their boots stomped by Jim's head by a matter of inches. She held her breath and watched as the got nearer to Albright's location. She could see him shaking from her location, his eyes bright in the dark.

Jim waited with baited breath as they continued to walk and sighed with relief as they left. She was surprised they hadn't heard her heart pounding. After waiting another ten minutes she signaled to Albright and they moved on in a modified route.

After three more hours she decided to set up camp. An overhanging rock face provided ample shelter and it was hidden. Albright immediately laid down and Jim struggled to suppress her glare.

"Got anything to eat, Kirk?"

Ok. Now she couldn't suppress her glare. She flung her pack on the ground next to him.

"There's some berries in there I picked yesterday. Get a small fire started and I'll be right back with some more wood and water."

Jim grabbed her rope, water canteens and knife. She stormed off with a huff and barely restrained punching him when he asked if that was all they had.

A quick wash in the creek and Jim felt refreshed enough to deal with whatever was thrown her way next. She'd even been lucky enough to spear a fish and find a good amount of dried sticks.

The way back to their camp had uneven ground that made her boots slip and as soon as she got close she knew something wasn't right. She crouched behind a fallen tree and scanned the campsite. Her pack was strewn across the ground, contents everywhere. A large campfire was burning and areas of the grass were flattened and torn up. Albright had been captured. Jim debated grabbing her pack but the crack of a twig nearby made the decision for her.

She needed to plan. Even though Albright was a prick and an idiot, he was still her team mate. She moved further up the creek and set up her trap. All she had to do now was wait.

Oooooooooooooo

Alexander Marcus was watching the feeds to the SERE training. It was always an interesting challenge for young cadets to complete the course but this particular group were more intriguing than usual. He sipped his coffee and replayed the last six hours of video when he had to pause in shock and surprise.

He watched as a young blond girl carefully set up her camp but with some...interesting modifications. She darted around and set a loop of rope tied to a tree branch, covering it with leaves. She then took off her jacket and hat and secured it around an upright log. After stuffing it with leaves to resemble a humanoid shape she looked at it from behind. She tilted her head and shook it before pulling her knife out and cutting her ponytail above the tie. The cadet then stuck it under the hat of her make-shift dummy before starting a large fire.

She was making a large amount of noise, shuffling leaves and breaking sticks before her head suddenly snapped up. It reminded Marcus of a deer detecting a hunter but with the confident movements, she was more like the hunter rather than the prey. The girl quickly tucked herself behind the trees and next to her rope. Marcus frowned and quickly smiled in interest as the two trackers hired for the course stepped out.

His coffee sat forgotten as he watched the takedown of some of Starfleet's best at the hand of a mere wisp of a girl. It was almost like a synchronized dance. Abey Sigo was quickly hoisted into the air by his foot and before Commander Phillips could react Kirk had the dropped weapon trained on him. A lesser man would have cringed at the dangerous glint in her bright blue eyes.

"Drop it!" Kirk ordered. A flash of teeth showed her satisfaction when Phillips let his rifle drop and kicked it to her. His eyes were wide in surprise. The blond didn't touch the phaser at her feet. Didn't even flinch as Sigo's fingertips brushed her back in his attempt to grab her. She merely stepped out of the way but kept her eyes and pilfered weapon trained on Phillips.

"Where did you send Albright?" She asked politely but her stance read hostile.

Phillips looked to Sigo for an answer and received a a shrug. Kirk jerked her rifle in a gesture of impatience. Marcus knew Phillips was thinking hard. Never had a cadet fought back and captured the team tracking them. There wasn't a protocol set for it. It wasn't what the exercise was designed for.

"We're just for tracking and capture. Once we tag you then you're beamed out. I'm not sure where." He answered. The blond nodded.

"Ok." She pressed the trigger and Phillips dropped to the forest floor stunned. She spun around and stunned the hanging man and cut him down. Marcus watched her raid their pockets for their food and take Phillips's jacket before leaving. He had to give her points. She was savage but at the same time civilized.

He pressed his comm button and smiled. He was impressed.

_"Yes, Admiral?"_

"Put me through to Fitzgerald. I have a cadet I want to discuss with him."

_"Aye, Sir."_

It wasn't long before an older gentleman's round face popped up on Marcus's screen. His eyebrows were drawn down in confusion.

_"Alex."_ He greeted.

"James." Marcus returned it with a nod.

He took a deep breath and leveled Fitzgerald with a smooth expression.

"I take it you've been watching Kirk's training feed?"

_"An interesting development to say the least. I've been watching from the beginning. I see loyalty to her team and ingenuity with what little resources she had available. Creativity and impressive tactics, too."_

High praise from Fitzgerald. He was a fool though. He didn't realize just what he was truly seeing. Marcus knew though. He saw a weapon in it's rawest stages. A tool that would be useful even though it had the impurities of concern and conscience but even that weakness could be exploited.

Marcus nodded and placed his hands on his desk, steepled his fingers and leaned forward.

"I'm curious as to her full abilities. I want to up the ante and bring her in. I'm thinking she can handle more than what this course originally intends, don't you think?"

Marcus watched as the other man frowned and shook his head.

_"I don't think so. This course is meant to empower cadets not break them. She'll go through the basic interrogation at the end and that's that."_

Marcus folded his hands on the desk and shifted in his seat, making sure his admiral stars were visible to the captain on the other end of the line.

"I was calling as a professional courtesy, James. I want to see how she responds. I need to know who I may be working with in the near future. I'm sending one of my men to take over. Marcus out."

He hit the button to disconnect, the screen flicking to black on the outraged captain. He had been wondering about Kirk ever since his nephew's difficulties last year with her. He had been surprised when he saw her file and it made for interesting reading. Kirk may be more useful than he had originally thought. The child she had had been a deterrent in his mind but looking at her now it may be worth the added baggage to have such a resourceful officer.

He knew about her Tarsus experience and had read the reports so he knew the standard interrogation at the end of this course was too easy. She needed a challenge. He needed to test Kirk's limits and raise the bar higher. He typed in his orders and sent them off. Leaning back in his chair, he started the feed and set it to play in the background. It was going to be an interesting week.

Oooooooooooooo

It was late evening and Jim had spent the past two days on high alert. She was finally at the edge of the beam out point. Suspicion was blooming in her gut at the utter lack of people at the retrieval area. With little to go on, Jim had no choice but to get to the co-ordinates. It had been a long, grueling two weeks in the forest. She missed Ella and she missed Bones.

At two, Ella was getting to be quite a handful. Jim wondered how McCoy was handling it by himself. The night before Jim's training had begun had been difficult to say the least. Bones had forgotten to keep Ella's food separated and had forgotten her purple puppy at daycare so she wasn't too happy. It had been her first night without it and it had taken hours to settle her down. And then...after all that, he had wanted to talk. The past few months he'd been hinting at moving in with them. It wasn't that Jim didn't want him there. It was more like she needed the space sometimes.

She wasn't used to living with someone else other than Ella and the idea of having another person there all the time was unnerving. She was also afraid that he'd grow bored with her or change his mind when he got to know her better.

The whole domestic lifestyle was still new to her and he'd seen some of her more unsavory behaviors. The first night McCoy had spent the full night with her he'd ended up with a black eye and a busted lip. Her nightmares had been more frequent since Finnegan and since then she'd been working herself to the point of exhaustion to keep the nights dream free.

Bones had a tendency to worry too much and to nag her into submission. It was funny sometimes but irritating others and Ella was picking up on McCoy's habits in her own way. When Jim was studying and forgot to eat then she would worm her way onto her lap to where Jim couldn't continue. The thoughts of home warmed her and made her smile. She knew Bones was going to have a fit when he got his hands on her and it was going to be soon. It was strange that she had managed to get to the beam out point without being captured by the "enemy". In all of her reading, that had never been documented but she was glad it was over.

With one last sweep of the area Jim hoisted the phaser rifle and ran out from her hiding place, her feet crashing through the undergrowth. She kept her pilfered rifle at the ready and as she arrived she hit the button on her wrist signaling for transport. The feeling of dematerialization took over and she sighed in relief. The forest around her fading to be replaced with a dark room and three figures in black. Jim saw the weapons pointed at her and didn't even have time to raise her own weapon before searing pain turned into black.

"Ah shi-"

**oooooooooooooooooooooooooooooooooo**

**AN: Hi all! I am so sorry for not updating sooner! This story needs a title so I'm shamelessly begging for title suggestions. This story is set during the end of Kirk's second year. It's a sequel to "Don't I Know You?" And focuses more on adventure than on getting to know the characters. Ella us now a vibrant two year old, McCoy and Jim have been together a year and this is my version of how Kirk receives the Palm Leaf of Axanar Medal for Valor. **

**I hope it's alright and I live for reviews!**

**Tishbing**


	2. Chapter 2

Chapter Two

Leonard McCoy frowned and stirred his coffee. Jim was supposed to have been back from her training three days ago. Horrible scenarios were running through his mind making it difficult to focus. He knew that she had a window of another twenty-four hours before she would be retrieved but that did little to assuage the gut-churning worry festering within him.

"Daddy, when's mommy coming home?" Ella climbed up into his lap at the table, her wide blue eyes shining with tears and worry for her mother. It had been hardest on her. Lately, she had taken to crawling into bed with him and had started having separation anxiety when he dropped her off at daycare.

When Jim's SERE training was set to start they had set up a calendar to cross off the days until her return but once the expected date passed Ella had started to become withdrawn. She'd even started sucking her thumb again.

McCoy ran a hand through her long, wavy hair and pressed a kiss to the top of her head.

"Soon, baby girl. I promise." He assured her, hoping he wasn't lying. Thumb tucked securely in her mouth and Pup Pup, her treasured purple stuffed dog, tucked under her arm, she curled into her father's arms.

He stroked her back and Ella snuffled into his neck. She was already emotional this morning and he knew that it was going to be a rough morning.

"Come on, kiddo. We've got to get ready." He stood but Ella's grip on his neck was strong enough that he was forced to carry her to her room. The past three days had made him proficient at doing things one handed with Ell on his other arm. He quickly pulled out a sundress and sandals from the closet along with a pull-up.

"Ok, let's get you ready." McCoy said in a falsely cheery voice but the small child shook her head forcefully and gripped his shirt tighter.

"Ell, you know Miss Daro will miss you at daycare. Today, Admiral Archer is bringing in his new litter of puppies. Don't you want to see them?"

He felt her slowly nod and climb down and McCoy sighed with relief when she put her arms up to let him get her dressed.

Oooooooooooooo

McCoy was thankful for the distraction of the two beagle pups in the daycare. Ella's face lit up and she was instantly smitten as the smaller of the two started licking her face and helping her forget for a time that her mother wasn't there. After giving Daro a nod he turned and headed to Captain Pike's office. He still had two hours before his ethics class and he wanted to see just where in the hell he'd sent Jim.

McCoy made his way across the campus, the walk doing little to calm him as he started up the stairs to Archer Hall. He'd seen cadets return from their SERE training in the medical center and he thought it was a barbaric practice. Survive, Evade, Resist, Escape. They came back sobered and with various bruises, burns, signs of exposure but they always came back at the three week mark. It was now day twenty-four.

The halls were bustling with smiling cadets but once they caught sight of McCoy's expression they quickly cleared the way. The administrative halls were more deserted causing the sound of McCoy's boots clicking on the marble to echo eerily.

He could hear angry voices coming from the office at the end of the hall. More importantly from the Commandant of Cadets office. Pike's voice as well as that of another man were clearly audible. Frowning, he listened closer and heard a third voice joining in arguing against the first two. The words were muffled but McCoy clearly heard Jim's name as well as a John Albright's name. He was about to knock on the door when a gray haired man with captain's stripes stormed out past McCoy without a glance. He was watching the older man out of curiosity when Pike's voice brought him back to the present.

"Cadet McCoy, I assume you're here to enquire about Cadet Kirk's whereabouts."

Pike gestured for him to go into the office and McCoy complied with an affirmative grunt.

Once the door closed, Pike dropped his formal attitude but his back was still ramrod straight with tension and his gray eyes gave away how worried he was.

"Where is she, Pike?" McCoy knew he was being insubordinate but right now he didn't give a damn. It was because of Pike that Jim felt that she had to push herself to the point of exhaustion to prove herself and it was Pike who had set Jim's course load to include some third year courses that most cadets wouldn't do until next year. Trying to cram a four year course into three with a sub specialty in Engineering was ridiculous. Factor in a toddler, it's a recipe for disaster. There were days that McCoy would have to resort to using Gaila to program Jim's PADDs to time out to get her to sleep or eat and even then he would sometimes have to resort to pharmaceuticals to force her to sleep more than an hour.

Pike raised his eyebrows at McCoy's tone and sat down behind his desk while the doctor remained standing, arms crossed at his chest, fully on the offensive.

"You know she's on her training mission. That man that just left was Captain James Fitzgerald who oversees the course. Currently, her training level was upped to special ops. As you probably heard we weren't too happy about it."

McCoy's hands dropped to his side in fists, his face flushing red in anger.

"The hell? She's command track not special ops! Who authorized the change? She's not ready for that level of training as a second year cadet! Aren't you supposed to be her academic supervisor? Pull her from the course! Don't you give a damn what could be happening? She's clearly missing!" McCoy shouted and thrust a finger at him accusingly. Pike stood abruptly in response, his chair scraping and clattering behind him in his rush to stand.

"Cadet McCoy, I allow certain familiarity with you because of your association with my goddaughter and because we both care about her but I will _not_ tolerate this level of disrespect." The commanding tone sobered McCoy slightly but inside he still seethed. His mouth snapped shut with an audible click but his jaw remained clenched in irritation.

"I am just as worried as you are. She's off the radar right now. This portion is part of classified level training ordered by Admiral Marcus. There's not a god damn thing I can do but I've been assured that she should be finished within the next twenty-four hours."

Pike's eyes flashed at the mention of Admiral Marcus and McCoy had to think why the name rang a bell before it hit him.

"Wasn't he the bastard that got his nephew Finnegan off the attempted rape charge leveled against him by Jim?" He asked with a scowl. Pike nodded and ran a hand over his face tiredly.

McCoy opened his mouth in outrage only to be silenced by Pike's hand forestalling the inevitable outburst.

"I know what you're thinking, Leonard and and I know Marcus. He's not doing this out of revenge. He's doing this because he sees something he admires in Kirk. I don't agree with his methods but he's a respected admiral." Pike gripped McCoy's shoulder, his grey eyes suddenly bright.

"I promise she'll be back before you know it." He smiled at the doctor, a knowing glint in his eyes. "And if I know Jamie, she's giving them hell."

McCoy snorted. "Damn straight."

Ooooooooooooooo

Jim felt like hell. Her entire body was in pain. The small smock they had put her in did little to warm her on the cold stone floor she was curled into a ball on. She could hear Albright whimpering next to her but he looked in good condition compared to her.

Mentally cataloging her injuries, she knew Bones was really going to kill her. Her left shoulder had been dislocated twice, left eye swollen shut, her ribs were killing her with every breath and she knew her urine shouldn't be pink. Her wrists were abraded from the shackles they had placed on her and her right wrist was possibly fractured. She was glad the drugs they had used on her had also worn off. This was not what she had been briefed on.

Since her wrist was too swollen for the cuffs, her "interrogators" had decided to attach one to her ankle. Bad move for them. She had been watching and waiting, Albright had been little help but he did relay that he had seen a transporter room. The small room they were in was simple, no electronics of any kind and since Jim's interrogators had been male, she used it to her advantage. There was a time and place to be defiant and after six days...this wasn't it.

It wasn't too hard to play the part of the broken female and as a result the amount of guards sent to retrieve her had been reduced to two. It was almost time.

"Albright? You with me?" She whispered.

A whimper was her answer.

"They're coming in a minute. I'm going to need your help. Can you walk?"

She saw him nod slightly and Jim breathed a sigh of relief. He'd better be able to walk if she was going to pull what she was planning off. His levels of "resistance training" had been what Jim had been expecting so he had a split lip, some bruising and that had been about it. His had mostly been psychological. He'd been forced to sit in one session and only Jim's defiant attitude had kept him calm.

The click of the old fashioned lock was loud enough to give her warning as she went limp on the ground. Rough hands touched her leg where she was shackled and then pulled her up.

"Come on, princess. We're gonna try one last time." A mocking voice was holding her up and Jim remained slumped, head lolling.

As soon as she felt him move, she struck. Spinning, she sucker punched the guard and quickly got behind him as the second man fired his phaser hitting the first guard square in the chest, stunning him. Jim shoved the stunned guard at his companion causing him to stumble and drop his weapon. Adrenaline surging, Jim dived for the gun. She couldn't feel her pain anymore, she just felt the high of endorphins as she twisted and fired blindly.

A loud thump let her know she hit her mark. She knew she had maybe ten minutes before anybody noticed what she had done. Grabbing the keys, Jim tossed them to Albright while she stripped the smaller guard of his uniform. Her movements were sluggish and difficult but she managed and it helped when Albright quickly understood what she was planning.

"Get dressed and grab the spare phaser. I need you to pretend you're one of them and get us to the transporter room."

The blond man's eyes were wide and he was frozen with either fear or uncertainty. She didn't care which. "Now!" She snapped and he leaped into action. Jim palmed the extra phaser and hid it in the folds of her smock and Albright pulled the cap on the uniform low enough to hide his face as he followed Jim out of the room and locked the steel door behind them, hiding their subterfuge.

"Third door on the left, around the corner." He whispered and Jim nodded.

They had just gotten to the corner when loud shouts from behind them alerted them that they had been discovered.

"Run!" She shouted and shoved the blonde man in front of her and she whipped out her phaser. Her aim was abysmal with the damage to her arms but it was enough that they were covered. They ran into the transporter room and immediately, Kirk pulled the side panel to the door off and ripped the wires.

"Seal that door!" She ordered. Once the whine of the phaser was heard melting the sliding doors together she turned to the transporter controls. Jim thanked Gaila for her tutoring in engineering and quickly powered up the unit, placing firewalls to stop anyone from powering it back down.

"Get on the pad." Jim looked up and Albright was watching her with a hesitant expression.

"What about you?"

"I'll be fine." She tapped in the co-ordinates for Starfleet medical and both their heads snapped around at the sound of banging on the door. Albright looked like he was going to jump off the pad but before he could move, the golden swirls of the transporter beam caught him and spirited him away.

The sound of phasers firing on the other side of the door made Jim smirk. Those things were solid tritanium. It'd take at least 10 minutes before a dent was made. Plenty of time.

Kneeling down, Jim starting pulling wires and twisting the cables. A few singed fingers was a small price to pay and she stood after five minutes of careful rearranging. Her heart started thumping erratically as she typed in the sequences needed. Her codes were starting to take effect and she heard the hum of the transporter pad powering up for it's second and soon to be final round. She set the phaser she still had to overload and stuffed it in the console, it's whine rapidly overtaking the transporter and ran to the pad.

As she felt the pull of her molecules being taken away she saw the doors open and guards filing in. She smiled and flipped them off. She was glad she had the pleasure of seeing their shocked faces as they saw her and then figured out the phaser overload. They had time...if they ran.

**AN: I want to give a big thank you to macywinstar who came up with the title "Hidden Agenda". Thank you so very much and as usual, Thank you for reviews and I really appreciate hearing from readers.**

**Tishbing**


End file.
